The Wrath of Kanaan
by nherbie
Summary: Kanaan is less than pleased with the relationship between Teyla and Lt. Colonel John Sheppard and decides to do something about it.
1. Chapter 1

A/N – This is not my first fan fic but it is my first sci-fi one, so here goes! If you got a notification and were expecting a wedding story for another series, I'm sorry! It's on the radar, I promise! This story just showed up and demanded my attention.

A/N2 -Typical disclaimer, I own none of the Stargate Atlantis characters nor the Star Trek movie, Wrath of Khan. If you liked the character of Kanaan, you won't like this story. I found him to be beyond bland and then he just faded into obscurity. I would put this story at post season 5. How I wish there had been such a season!

~,~,~,~

Chapter 1

"Colonel? Could I have a word with you please?" The voice was soft, almost hesitant, and it brought a grimace to John Sheppard's face. He carefully plastered a pleasant smile on his face as he stopped and turned to face the man who'd addressed him.

"Hey, Kanaan. What can I do for you?"

"I was wondering if you would do me the honor of sparring with me this afternoon? Bantos rods?"

That was the last thing John wanted to do but he knew Kanaan was making an effort to fit in here on Atlantis and he also knew that Teyla was concerned about him. What he didn't want was for her to take it into her head that she, Kanaan and Torren would be better off on the mainland with the rest of the Athosians, he would miss her and the child too much. While she was now totally out of his reach, he couldn't imagine her not being in his life. So, he had to find a way to make nice with the man who had what he wanted, something he'd finally realized, only too late.

"Sure, if you want to. I get off duty at 1500 hours, shall we say 1530 in the gym?"

"That would be fine. I will see you then." Kanaan hid his triumph behind his bland smile and walked away. Teyla was _his_ and this trumped up military officer from another galaxy was not going to interfere in any way. He'd been working on this plan for a while now, ever since he realized that he'd retained some of the Wraith like powers that Michael's experiments had given him, and he was now finally ready to set that plan in motion. It had begun.

~,~,~,~

John stepped into the gym, exactly on time, to find Kanaan already there and waiting. He swallowed a sigh, not wanting to admit just how much he'd hoped the other man would either forget or just blow him off. If he was anywhere near as good with the Bantos rods as Teyla, he was probably about to get his ass kicked and he already had a headache. He moved to the bench and threw his gym bag down, pulling out his personal rods that Teyla'd given him for his last birthday, not seeing the look of pure hatred the other man was throwing his way. Kanaan was well aware of just how much care and effort she had put into obtaining those rods, they had had to be exactly the right length and weight, perfectly balanced. Pair after pair were inspected and discarded until she'd found the perfect set. It had been readily apparent to him that this was not the gift of one friend for another. He, himself, had never been interested in this form of fighting and barely knew which end of the rod to hold. When John turned back, he had the bland smile back in place and concentrated on the next part of his plan. Satisfied that things were moving along nicely, he bowed to the Colonel as the man bowed to him and they began to circle one another.

When Kanaan felt the familiar presence approaching the door, he feinted a move towards the Colonel who parried it. Deliberately, he left an opening that the Atlantean used to lightly tap him on the shoulder. He went down, dropped his rods and threw his hands up just as Teyla and Ronon came through the door. "No more Colonel! Please, I do not understand what I have done to anger you so!"

"Kanaan? John?" Teyla asked as she hurried to the downed man's side. Kanaan looked into her eyes and concentrated, splitting his focus on her, the Colonel and Ronon. John's headache just ratcheted up a notch but Ronon's eyes narrowed to glittering slits as he moved to protectively hover over Kanaan and Teyla. Teyla took in the condition of her mate and felt a rage rise within her.

"What are you talking about?" John asked in surprise. "I barely touched you once, we'd only just begun to spar!"

"Is that what you call it? Sparring? I came here at _your_ request to learn to use the Bantos rods, something I did only to please Teyla and you viciously attacked me!" Kanaan responded.

John continued to stare at him in shock and then turned his eyes to Teyla. She was glaring at him and gently stroking Kanaan's hand. "John, I thought better of you! You know Kanaan is not interested in fighting, why would you do this?"

"I didn't! _He_ asked _me_ to spar with him, I didn't even want to except I thought it might be a way of making him feel like he fit in here!"

"That is a lie! Why are you doing this Colonel Sheppard?" Kanaan asked from his seat on the floor. He was a little surprised that the man wasn't succumbing to his suggestions like Teyla and Ronon were. He should have been acting more aggressively, making himself appear even more appalling in the eyes of his two teammates.

"Why would I lie?"

"I have no idea John, but we need to get Kanaan to the infirmary immediately. We will talk of this later!" Teyla helped Kanaan to his feet and he leaned on her as if he was in great pain.

John went to follow them when Ronon stepped in his way. "I thought better of you Sheppard!" He spat out.

"Look, Ronon, buddy, I'm telling you the truth, I came here at his request and I barely touched him!"

"I know what I saw, Sheppard, and if that's your idea of barely touching someone, I'd hate to see what you consider a beating!" With that parting shot, Ronon left the room, catching up with Teyla to offer his support in assisting Kanaan.

John just stood in the middle of the now empty gym with his mouth slightly open, not sure exactly what had happened. "What the hell?"

~,~,~,~

Jennifer Keller was on duty when Ronon and Teyla brought Kanaan in. When she heard that he'd been injured in a fight with Colonel Sheppard, she frowned. That was not like the man she had come to know since becoming the CMO of Atlantis. She had always found him to be a fair man, with a wry sense of humor that she thoroughly enjoyed. She just couldn't imagine what would have made him attack the man lying on the gurney in front of her. She lifted his shirt while he concentrated on her. Gasping, she pulled back. "My God, how many blows did you take?" Almost all of his torso, arms and legs were covered with burgeoning bruises, new ones almost appearing as she looked. His face was bruised as well.

"More than I wanted. If Teyla and Ronon had not come in when they did, I shudder to think what Colonel Sheppard might have done to me." Kanaan gave her the most bewildered look he could.

"I want to get you under the scanner, make sure he didn't do anything more than bruise you!" Keller pulled the shirt back down over his abdomen and patted his arm.

"Thank you Dr. Keller."

"It's Jennifer, Kanaan."

He inclined his head. "Then thank you Jennifer."

She smiled at him and then called one of the nurses over. "Marie, can you get the scanner ready? Kanaan had a run in with Colonel Sheppard and I want to be sure he didn't do any damage internally."

"He what?" Marie had spent more than her fair share of time with the Colonel when he was hurt and laid up in the infirmary. She genuinely liked the man and thought this sounded very out of character. Kanaan concentrated on her as he lifted the hem of his shirt, exposing the bruises. "Oh my, I can't believe the Colonel did that to you! How awful!" She hurried away to get the scanner up and running, wanting only to alleviate the pain the man was so obviously suffering. Her opinion of a certain messy haired colonel doing a complete one eighty.

Once he was under the scanner, Jennifer and Marie watched the results. Jennifer shook her head in disgust as she registered the cracked ribs and internal bruising. She turned back to the trio waiting for her. "He has three cracked ribs, luckily none are broken. There doesn't appear to be any internal damage other than bruising. I can wrap your ribs and give you some pain medication but that's about all I can do."

"That will be more than enough Jennifer. Does he have to stay here or can he return to our quarters?" Teyla asked.

"He can go with you, but keep a close eye on him for the next twenty-four hours. If you see anything that concerns you, please, tell me right away."

"Of course."

Jennifer gently bound his ribs, giving him a shot for the pain. Marie gave Teyla some pain pills with strict instructions on their use and then he was finally ready to be released. He stood and swayed a little, causing both Teyla and Ronon to rush to his side. He gratefully accepted their help, suppressing his smile at how easily they were all fooled. On their way out of the infirmary, they ran into a group of four marines who knew Teyla from sparring with her. Asking what had happened, they too were stunned at the unexpected news that their CO had attacked Teyla's mate, although they each had their own sneaking suspicion as to the why. No one who saw the two of them together, could miss the electricity between them, no one but the two of them it seemed. As Kanaan concentrated on the four men, he noticed with pleasure that one of them was making a fist. He nudged that man a little more as they took their leave. Behind them, Jennifer put in an irate call to Richard Woolsey, leaving no room for misinterpretation of what her current opinion of the commanding officer of the base was.

Walking slowly back to their quarters, they also ran into Dr. McKay, who was looking for Sheppard to activate some ancient device or another. Kanaan's lip curled as he realized the man expected to find the Colonel with Teyla and Ronon, like they didn't have separate lives. He concentrated on McKay and was surprised to see the other man frown but not fall all over himself, condemning the Colonel for his actions as Teyla explained what had happened.

"That doesn't sound like Sheppard at all!"

"I know what I saw McKay!" Ronon growled menacingly at him.

"Down Conan, I'm not saying you didn't see it, just that it doesn't sound like something he'd do."

"Doesn't it? How well do you really know him?" Asked Ronon.

"I would say very well, as I would have expected both of you two to say as well."

"Well, the man who did this is not someone I know at all." Teyla retorted angrily.

Rodney frowned and looked at Kanaan who merely returned his gaze with one of bewildered sorrow, artfully portrayed. The scientist finally nodded at them and went on his way. Back at their quarters, Teyla and Ronon hovered over him, getting him anything he asked for. He could get used to this. He closed his eyes and sent out a broader cast, no longer needing to influence anyone into seeing what wasn't there, just influencing a general feeling of dislike for the Colonel. All across the city, people either clutched their head at the sudden pain of a headache or frowned as their thoughts turned inexplicably to John Sheppard and how very much they didn't like him.

~,~,~,~

Jennifer looked up when she sensed a presence behind her. She turned with a questioning expression on her face, one that turned to disgust at the man in front of her. The look on the CMO's face surprised him. Frostily she asked. "What can I do for you, Colonel Sheppard?"

Hesitantly he said. "Hey doc, I need something for a headache. Can you help me out?" Normally he would never admit to pain, but the headache had increased to near migraine proportions and was starting to make him nauseous. His confusion about what had happened earlier this afternoon was not helping matters.

Jennifer sighed and stood up. She'd prefer to just let him suffer as he'd made Kanaan suffer but it went against all her principles. She opened the medicine cabinet and took out some aspirin. Without a word, she thrust them at him and then turned her back. He frowned at her, wondering what he'd done to her but then shrugged. He needed to get the pain under control before he could sort this all out. He dry swallowed the aspirin as it was apparent she was not going to offer him any water. He stared at her back for a moment and then said quietly. "Thanks Dr. Keller." He turned and left Jennifer stewing in anger behind him.

He stepped out of the infirmary just as his comms chirped. "Colonel Sheppard, can you please report to my office immediately?"

"On my way Richard."

"Mr. Woolsey, please."

John sighed, not him too? He made his way to the control room and passed through on his way to the expedition leader's office. Normally, everyone on duty would have a word with him, now they all studiously ignored him or actively sent him looks of disgust. He rolled his shoulders, feeling eyes on his back. He made it to Woolsey's office and knocked before entering.

"You wanted to see me, Mr. Woolsey?" They had long ago progressed to the stage of John and Richard, but that had obviously changed somehow. Woolsey finished what he was doing, making the Colonel stand in front of him, waiting. The dislike he currently felt for the Colonel surprised him, he'd always gotten along well with the man. He remembered his first days as leader, having just replaced Samantha Carter. He was sure the Colonel would be combative, as it was widely known that the two got along well and she was military like Sheppard, whereas he would be considered by many to be a bureaucrat. Things had gone badly quickly when Dr. Keller had been taken over by an alien entity and the city was in danger. He'd made decisions that went against every fiber of his being, decisions that had had to be made. He'd stood next to the Colonel's bed in the infirmary when it was all over and admitted he wasn't sure he was cut out for the job, that he'd broken so many rules in such a short time. John Sheppard had just grinned and held out his hand, saying 'Welcome to the Pegasus Galaxy.' They'd worked well together since then but the current situation would not, and could not, be tolerated.

"Yes, Colonel." He didn't request that the man be seated and he watched as Sheppard warily went into parade rest in front of him for the first time ever. "Dr. Keller filled me in on a very disturbing incident between you and Kanaan. I have no idea why you would attack a civilian in such a manner. I understand he was very badly hurt."

John blinked a couple times. "How badly was he hurt? I tapped him once on the shoulder, and lightly at that! If he has other injuries, he didn't get them from me."

"Dr. Keller says that Ronon saw the whole thing and was most upset that you had beaten up an innocent man."

"I don't know what Ronon saw but it wasn't me beating up Kanaan! Why would I do that?"

"It's pretty obvious Colonel, even to me, that you have feelings for Teyla. Interesting that her mate was the one you brutalized, isn't it?"

John's face flushed a dull red and then the blood drained out of his face, leaving him white as a sheet. Were his feeling for Teyla that evident? He'd thought he'd hidden them successfully. They still worked well together and he made sure he didn't treat her any differently from the rest of his team. "I have no idea what you're talking about sir, and I didn't brutalize him!"

"Well, I can't ignore such a serious complaint. Effective immediately, I am relieving you of command while we sort this out."

"You're what? You can't do that!"

"You heard me Colonel. I'm well within my rights, as expedition leader, to remove you from your post if I feel you pose a threat to the city or its inhabitants."

"Pose a threat? Me?"

"Dismissed."

"Sir, this is wrong, you know I wouldn't do something like this!"

"I'm afraid I know nothing of the sort, Colonel. Major Lorne will assume your duties while we investigate. Should you be found innocent of any wrongdoing, your command will be reinstated. If you are found guilty, I will request you be removed from Atlantis and sent home for punishment."

John felt like he'd been shot. Leave Atlantis? This was his home now. He couldn't imagine living back on Earth. Leaving his friends behind. Suddenly it struck him, he wasn't sure he had any friends here after all. He nodded once to Woolsey and walked from the room, trying to be dignified but really wanting to bolt, to race away as his life crumbled around him, totally out of his control.

~,~,~,~

Relieved of duty and bewildered at the turn of events where two of his closest friends and teammates had refused to believe his version of what had happened, followed quickly by the actions of the Chief Medical Officer of the base, someone he'd also considered to be a friend, John found himself at the East Pier. This was the place he went when he had something to work out in his head. Unfortunately, the aspirin had made hardly a dent in the pain and he leaned his forehead against the wall, letting the coolness sooth him. He heard footsteps behind him and turned to see Rodney headed his way, staring at his tablet as always, not paying attention to where he was going. John waited until he was right on top of him and then asked warily. "Rodney, what are you doing down here?"

Startled, Rodney looked up at his friend and grimaced. His head hurt and he just wanted to complete his mission before heading to see Jenn about some aspirin or maybe something stronger. "I was looking for you. I need you to activate something Radek and I found. I called you a couple times but you didn't answer. I had to follow your sub-q transmitter to find you. What are you doing down here anyway?"

"Just needed to do some thinking."

"Yeah, I heard you had some kind of fight with Kanaan? I saw him leaving the infirmary with Teyla and Ronon. I have to say, he didn't look too hurt to me."

"According to Woolsey, I brutalized him. To the point where I've been relieved of duty pending a full investigation. Lorne's now in charge."

"You're what? Why would he do that?"

"Dr. Keller lodged a complaint against me."

"Jenn did that?"

"Yeah. Look, Rodney, I'm not really in the mood for plug and play right now, plus I'm not sure Woolsey would approve. Apparently he thinks I'm a threat to the city."

"He's nuts!"

John sighed, relieved that at least one of his friends was still behind him. "I don't know what to think Rodney." He watched as McKay rubbed his forehead. "Headache?"

"Yeah, can't seem to get rid of it. I'm going to ask Jenn for some aspirin."

"If it's anything like mine, the aspirin won't help. I'm close to migraine at this point."

"You have one too?" At John's nod, he pursed his lips. "Hmm. I wonder if it's just a coincidence or if something's going on."

"You think this might be related to why everyone thinks I beat up Teyla's mate in a fit of jealous rage?"

"It might, you never…. Wait, did you just say jealous rage?"

"Woolsey pretty much accused me of that, yes."

"Wow. Huh. You and Teyla?"

"McKay! No, not me and Teyla. She's a member of my team, just like you and Ronon. With everything else that's going on, that's what you focus on?"

Rodney grimaced and looked back down at his tablet as if it would have the answers for him. He glanced back at John and noticed for the first time how drawn he looked. "Listen, why don't I go and talk to Jenn. I'll get my aspirin and see what I can find out about Kanaan's injuries. I'll fill you in afterwards."

"Thanks McKay. You have no idea how good it feels to have someone finally believe me." He held out his hand and Rodney shook it.

"We'll figure this out, we always do!" He turned and left to go talk to his girlfriend, leaving a tired and shaken Colonel behind him.

~,~,~,~

"Jenn?"

"Oh, hey Rodney! What's up?"

"I have a headache and was wondering if I could get some aspirin?"

"Sure thing! Just take a seat and I'll go get it." She bounced up and went to the medicine cabinet while he hoisted himself up on the side of a gurney. She came back with the aspirin and a paper cup full of water. He smiled his thanks and swallowed them quickly.

"So. I heard you had some excitement earlier?"

Jennifer frowned. "Look, Rodney, I know Colonel Sheppard is your friend, but you didn't see what he did to Kanaan. The man was just one big bruise, chest, back, sides, legs, arms even his face! And he has cracked ribs! I'm not sure I like the idea of you hanging out with him anymore."

Rodney stared at her, open mouthed. The Kanaan he'd seen walking out of here with Teyla and Ronon had shown no signs of bruising anywhere that was visible. And was his girlfriend really telling him who he could and couldn't be friends with now? He snapped his mouth shut, he needed to tread carefully for once. "I ran into Sheppard on the East Pier. He told me you lodged a complaint with Woolsey and that he's now relieved of duty."

"Good! A man like him shouldn't be in charge of anything!"

"Jenn? You used to consider John a friend, aren't you being a little harsh, not knowing exactly what's going on?"

"He's had everyone fooled! I think he's finally shown his true colors. I hope Woolsey sends him away from Atlantis for good! I don't feel safe with him around."

One of the nurses passed by, he thought her name was Marie or Maria or Marilyn, something like that. She heard the end of their conversation and stopped, her head nodding up and down, showing her agreement with everything Jenn was saying. He glared at her and she skittered away.

Turning back to his girlfriend, he thought about what she'd said and swallowed hard. He hadn't thought about what would happen if John were found guilty. He'd have to go back to Earth and would probably be court martialed. If not, then at least busted down in rank. His best friend would no longer be on Atlantis and he couldn't imagine anyone else taking his place. He couldn't imagine anyone else leading the war against the Wraith. He knew they wouldn't allow another Major to be commander so Lorne was out, not now that they were in constant contact with Earth. He tried to imagine Atlantis under the command of someone like Caldwell and shuddered. He needed to figure out what was going on and figure it out now. He hopped down off the bed. "I'll think about what you've told me Jenn, I will. I just have to wrap my head around it."

She took a quick look around and saw no one was near. She kissed him hard and said. "You do that, I know you'll come to the right decision."

He smiled sickly at her and started from the room. Reaching up, he touched his comms and said quietly. "Major Lorne, this is Dr. McKay."

"Yes Dr. McKay."

"I need to see you, right now!"

"There's nothing I would like better. Where?"

"I'm just leaving the infirmary, how about we meet in Colonel Sheppard's office? I just saw him down on the East Pier so I know he won't be using it."

"Works for me. He tell you what's happened?"

"Yes and that's part of what I wanted to talk to you about."

"Good, see you shortly."

Rodney nodded, even though Lorne wouldn't be able to see him. He paid no attention to the marine standing outside the infirmary, listening intently to McKay's side of the conversation. The scientist brushed past him without even noticing him. The marine smiled and turned to walk away. He had an idea and knew just who to include.

~,~,~,~

Rodney walked into John's office without knocking, as always. Lorne was waiting for him, sitting on the edge of the desk, refusing to sit in his CO's chair. He'd been on Atlantis for a while now and thoroughly enjoyed working under Sheppard. He'd initially been wary of how easy going and nonmilitary the man appeared to be, until the first time he'd seen action with him. Gone was the laughing, mischievous flyboy and in his place was a warrior with a keen sense of military strategy and a bravery that bordered on reckless disregard for his own personal safety. Some of the things his boss came up with were so far outside the box, they were in yet another galaxy. Still, his plans always seemed to work. He'd also discovered the man was fiercely loyal and never expected a member of his command to do something he wouldn't. In fact, he usually took the most difficult assignments on his own. Add in the fact that he, and his team, were trouble magnets, and he'd spent more time covering Sheppard's duties than he cared to remember and he found he didn't want the job permanently, especially if it meant disgrace for the man he'd come to admire and respect. If he could have refused to take command when Woolsey had informed him that Sheppard was relieved of duty, he would have, if only to show his support of his CO. He knew the Colonel wouldn't want that, so he'd reluctantly kept his mouth shut. Wearily, he rubbed his forehead, trying to lessen the pain.

McKay watched the motion. "Headache?"

"Yeah, can't seem to shake it."

"Well, I have one too and so does Sheppard. His was almost migraine level when I talked to him."

Lorne frowned at him. "Two of us could be a coincidence, three of us seems a little odd!"

"My thoughts exactly! Something's going on here Major, and it's not John Sheppard going off the deep end over Teyla's relationship with Kanaan! Jennifer told me that Kanaan was bruised from head to foot but I saw him when he left the infirmary. I saw no such bruising, although he was leaning on Teyla and Ronon like he was in agony."

"So, what's going on?"

"How the heck am I supposed to know? Do I look like a magic 8 ball?" Rodney grumbled, his voice rising in pitch towards the end, causing Lorne to wince. This would be about the time Sheppard would issue a challenge and he would feel like he needed to rise to it. When nothing was forthcoming from Lorne, he blinked a couple times, floundering. For his part, the Major suppressed the urge to yell at the doctor, his headache making him less tolerant than usual. He'd never understood how Sheppard could not only work so closely with the annoying and egotistical man, but actually count him as a good friend.

"You said Dr. Keller was convinced John did this. Did you talk to any of the other medical personnel?" Lorne didn't even realize he'd called his CO by his first name, his concern more for a friend than a commanding officer right now. Rodney, being clueless to the emotions of those around him, didn't notice.

"No, but Mara, Marcia, Marcy, whatever the nurse's name is, was there and looked like she agreed with everything Jenn was saying, just kept nodding. It was very annoying. It doesn't make any sense, why would they be so easy to convince? They've known Sheppard longer than they've known Kanaan, yet they sided with him without giving the Colonel any benefit of the doubt!"

"Do you think we should talk to Dr. Beckett?"

Rodney mulled it over. "It couldn't hurt. He wasn't there when Kanaan was brought in, maybe he'll have a more level head."

Lorne stood up from the desk and keyed his comms. "Dr. Beckett, this is Major Lorne, please respond."

"Aye Major Lorne, what can I do for ye?"

"Would you have a few minutes to talk with Dr. McKay and myself?"

"Of course laddie. I just came on duty. Why don't ye meet me here?"

"Thanks! See you in a few minutes doc." He looked at McKay who was staring off into space. "McKay?"

"Huh? Oh yes, what?"

"Dr. Beckett says he'll meet us at the infirmary. You ready to go?"

"Well, of course! I was waiting on you!"

Lorne closed his eyes and counted to ten. Opening them, he silently led the way to their meeting with the good doctor.

~,~,~,~

John stood on the East Pier and looked up at the evening sky. If he had to leave here, he would miss this life so much, he wasn't sure if he'd be able to stand it. All his life he'd felt like the outsider, never fitting in with his father and brother who seemed to breathe, eat and drink commerce. All he'd ever wanted to do was fly. His mother used to tease him that he was a changeling, a fairy child who was left in the place of the human child she'd birthed, born to spread his wings and fly away. The thought of joining the family business had actually caused him physical pain. His mother had been the only one he felt connected to in his family and, when she died when he was just a child, the connection was severed. He'd joined the Air Force over his father's strenuous objections, leading the old man to cut him off. He hadn't really cared, the money he and Dave seemed to worship, meant nothing to him. He'd made some good friends along the way, friends he'd then lost to war and to enemies who seemed to care nothing for human life. The first time he'd set foot on Atlantis and the lights had come on to welcome him, his first thought had been "I'm home." That feeling had never left him. There was no way he was going to leave here without putting up a damn good fight.

He found himself wondering if he could just disappear into the uncharted areas of the city and live the rest of his life here, staying one step ahead of those who would be looking for him. He had a feeling Atlantis herself would help him if it meant he could stay. He shook himself, smiling a little at the realization that he thought of the city of the Ancients as a she and sentient. There were times when he thought it wasn't that much of a stretch of the imagination, until Rodney would clue him into whatever code he'd uncovered that had caused the city to react in whatever way she had. He softly caressed the railing he was leaning against and could swear he felt an answering wave of affection. A sound behind him disturbed his reverie.

He turned a moment too late, his guard down as he'd been absorbed in his turbulent thoughts. The fist caught him full in the jaw, knocking him sideways. Two men grabbed his arms and another two began to beat him as he struggled and got in a few hits of his own. The fight moved this way and that on the pier but he was outnumbered. The last thing he remembered was being flung up against the wall, his head making a disturbingly moist thud as it bounced off. The world went black and he crumpled to the ground. He never felt the rest of the blows and kicks that the four men delivered. Eventually, they tired and, without a word, they walked away and left their CO a bloody mess behind them.

~,~,~,~


	2. Chapter 2

A/N - Thanks to my beta and friend, Honus47 for finding my mistakes. Any left are all on me!

A/N2 - I went a little overboard on Carson's accent, even resorting to googling a translate site. I've heard from several people that it makes it hard to read/follow, so I dialed it back significantly. Sorry about that!

~,~,~,~

Chapter 2

Carson looked up from the reports he was reading, a frown on his face, when Lorne and Rodney entered the infirmary. He got up and waved them into his small office, shutting the door behind them. Sitting back down, he rubbed at the ache behind his eyes. Having a headache at the beginning of a night shift didn't bode well for the rest of the evening. Lorne and McKay watched the movement and turned to each other. McKay was the one to ask his friend. "Headache?"

"Aye. Not to worry, I took some aspirin when I came on duty."

"We don't think it well help much doc." Lorne said.

Carson looked up with a question in his eyes that Lorne answered. "I have one, McKay has one and he says Colonel Sheppard told him he had one bordering on migraine. I think that's a bit much to be a coincidence."

"Aye, so it would seem." He once again frowned down at the report he'd started reading when he came on duty, catching up on the events of the prior shift.

Lorne watched him for a moment and then broke the silence. "Doc? We have a problem here. Woolsey has removed Colonel Sheppard from command and put me in charge. "

"Bloody hell! Why would Woolsey do that?"

McKay answered. "He thinks John is a threat to the city! Can you believe that nonsense?"

"Why would he think that?"

"It all appears to lead back to the incident with Kanaan." Lorne replied.

"Aye, I was just reading over Jennifer's report on it. It makes no sense."

"In what way?" Lorne asked.

"Well, first off, her report indicates that Kanaan was badly bruised and had three cracked ribs along with internal bruising. She used the scanner on him but the readouts from it indicate no damage at all! He's healthy as a horse. I don't understand how she could've misread this so badly!"

"Do you think she was influenced some way?" McKay asked.

"How?" Lorne and Beckett said at the same time.

"Well, I don't know! I mean, Teyla, Ronon, Jenn and Marjorie, Margo, Maryanne…why can I not remember her name?" McKay asked plaintively, getting distracted.

Beckett rolled his eyes at his friend. "I have no idea, Rodney! Her name is Marie and you've known her for over five years!"

"Well, it's not like we hang out or anything! I work with Zelenka every day and it took me almost two years to remember his name!"

"Rodney…."

Lorne interrupted them. "Uh, docs? Can we get back to the situation at hand?"

Both blinked at the Major and Rodney cleared his throat. "Yes, well, _they_ were all so bent out of shape about the condition Kanaan was in, I was surprised, and it didn't make any sense! I didn't see any bruises or anything else to indicate he was hurt, other than what he was telling people."

Beckett narrowed his eyes and thought for a moment, the other two watching him silently. A sudden thought had him reaching for his comms. "Dr. Beckett to Sgt. Stackhouse, come in please."

There was a moment's silence. "Yeah Doc, I'm here, what do you need?" The tenor of the man's voice indicated he was agitated.

"Just a quick question laddie. Do ye have a headache?"

"Yeah, I do. How'd you know?"

"I'm not sure just yet. Have ye heard about Colonel Sheppard?"

"I have! I can't believe it, I won't!" One of his first missions off world had ended up with the then Major Sheppard almost dying from an ugly bug that had attached itself to his neck. He and Markham had found out later that the man had refused to give up on them, even though they'd been demolecularized in the front part of the stuck jumper. He's been a firm Sheppard guy from that moment on. When Markham had died during the Wraith attack, his CO had gone out of his way to talk with him, knowing that the two had been best friends, quietly sharing his own memories of friends lost during war, something that had cemented his unadmitted hero worship of the man. "Look, what's going on? I've already gotten into fights with what feels like half the marines and air force guys here, all saying how it's about time he was relieved of duty! Some of them I've heard openly express their admiration for the Colonel in the past! What's with the sudden turn around?" His voice was becoming even more agitated.

"We aren't sure son, just….don't go 'n' get intae any more fights. We think someone or something is influencing people's feelings aboot John. 'Tis nae their fault." Beckett's Scottish accent tended to get thicker when he was upset.

"Then why do I still feel the same, other than the headache?"

"I'll have to get back to ye on that. Beckett out."

He looked off into space and then at the two men before him. "Major, what do you, John, Rodney, Sgt. Stackhouse and myself have in common?"

Lorne thought for a moment and the light went on. Before he could say it McKay exclaimed. "The ATA gene! We all have the gene, either naturally or artificially. John has the strongest and his headache is the worst."

"Aye."

"That still doesn't explain what's going on doc! Just maybe why we aren't impacted." Lorne said.

Carson frowned and went back to the scan attached to the report on Kanaan. He opened up additional scans and then paused at one, looking at it carefully and then raised his eyebrows in consternation. "Jennifer scanned his brain, looking for swelling or bleeds, and found none. But, check here…" He pointed to an area of Kanaan's brain that showed a darker color, the two other men leaning over his shoulders to look.

"What am I looking at, doc?"

"Yeah, Carson, I don't read voodoo!"

Beckett sighed. "That indicates increased synaptic activity in that area of the brain. That's unusual in humans but not…" He paused and pulled up a different scan, this one of Todd who had submitted to several medical exams at John's request. The dark area was the same. "…for Wraiths."

"Are you saying Kanaan is under the influence of the Wraith?" Lorne asked.

"No laddie, I'm saying the retrovirus I administered to reverse Michael's tampering, may have left him looking like a human again, but apparently left some Wraith characteristics behind. You know they can influence what ye see? Make it appear that there are more Wraith in the area then there actually are?"

"So you think Kanaan was given this ability and still has it? And he's using it to influence people's thoughts about the Colonel? He made the others see bruises and broken bones where there are none?"

"Aye, that's exactly what I think."

"And because we have the ATA gene, it makes us immune? Just gives us a bad headache?"

"Aye. Ye know Colonel Sheppard has never been fooled by the Wraith ghosts. The ATA gene must be why."

"Carson, do you think he's doing this deliberately or is it subconscious?" McKay asked.

"In all honesty? I think it's a deliberate attempt to remove Colonel Sheppard from Atlantis and get him away from Teyla. That would be the only explanation for the way he's acting. If he wasn't directing this, there would have been no need for the charade of John's supposed beating o' him."

"We need to report this to Woolsey and get the Colonel reinstated ASAP!" Lorne said, glad to finally know what was going on.

Carson held up a hand. "I don't think that will work, Major. From what ye've told me and what we just heard from Sgt. Stackhouse, Kanaan's influence appears to be quite strong and far reaching."

"Then what do we do?"

"I have a plan but I think, first, ye should get Colonel Sheppard into protective custody based on the things Sgt. Stackhouse said. He could be in danger from his own men."

Lorne nodded and keyed his comms on. "Major Lorne to Colonel Sheppard, do you copy?" He waited. When he got no response, he tried again. "Colonel Sheppard, please come in." Still no response.

Not to be outdone, Rodney keyed his as well. "McKay to Sheppard. John, answer me!" When he also got no response, he pulled out his tablet and opened the program he'd used to track John down earlier. "He's still on the East Pier, almost in the exact same spot I left him earlier." He stared at the screen for a moment. "He's not moving!"

"Don't get all worked up on us now, Rodney! Just because he isn't moving, doesn't mean something bad happened. He may just be sitting quietly."

"This is Sheppard we're talking about here Carson, he doesn't do anything quietly!"

"Why don't ye both go find out and I'll stay here to work on my idea." He paused and then said. "Contact me as soon as ye find him." His words showed he was just as worried about his friend as Rodney was. The two men left quickly.

~,~,~,~

Taking the transporter closest to where the scanner showed Sheppard was, the two men hurried through the corridors. They exited out onto the huge balcony where the program said he'd be, to find it almost pitch black, the only light that which was reflected off the water from those sections of Atlantis that were still lit. Thick clouds had moved in to hide the moons. Both flipped on the flashlights they always carried, even when they were on Atlantis, just as it began to rain. "Oh great, just we what need! Rain!" McKay grumbled. "Where the hell is he? The scanner says we should be almost on top of him!" He stated, giving his hand held tablet a shake.

"Let's split up and search, McKay, he's got to be here somewhere. You go left, I'll go right."

"Okay, fine. Just…don't get out of my sight, okay?"

"Sure thing doc." The two men split up and started searching, the meager light from their flashlights barely piercing the darkness. A few minutes later, Rodney almost missed it on his first sweep of the area. Damn the Colonel for insisting on wearing black BDUs, he blended right into the night.

"John?" He said tentatively, just knowing there would be no answer. He took a step closer. "John! Major Lorne, over here!" He gathered himself and sidled up to the unmoving figure lying on the ground, resting, almost hidden, up against the wall. His flashlight moved over the man's body and he almost gagged. "Jesus, John. What did they do to you?" His friend's face was almost unrecognizable under the massive amounts of blood and swelling, bruises covering almost every inch of exposed skin. "Lorne, we're going to need a medical team here!" Lorne came racing up and stared down at the beaten man at his feet. Reaching over, he put two fingers against the man's neck and sent up a silent prayer. At first he felt nothing and was afraid they were too late. He pressed a little harder and finally felt a faint pulse. He breathed a quiet sigh of relief.

Relying on all of his military training, Lorne forced his concern for his CO down and calmly keyed his comms. "Dr. Beckett, Major Lorne here. We have a medical emergency on the East Pier."

"Is it the Colonel?"

"Yeah, he's been beaten pretty badly. I can feel a faint pulse but it looks like he's lost some blood and he's barely breathing."

"On my way!" Carson bolted from his office and grabbed two of the night shift nurses. "Put together an emergency kit and a mobile gurney, stat!" Both of them nodded and moved like the well-oiled machine they were, asking no questions, just putting together everything they could possibly need in the shortest amount of time. Together they raced to the location, met by Major Lorne at the transporter. When they got to the Colonel, both nurses backed away when they realized who it was. "Bloody hell! Don't ye both dare to pull this on me right now! This man needs our help and, no matter how ye may feel about him, do yer duty!"

Both of them blinked and frowned, moving forward to assist the doctor. Beckett began to assess his patient. "Pulse is weak and thready. Decreased breath sounds on the right. He might have a broken rib that punctured his lung. We need to get him back to the infirmary and into surgery as soon as I have him stabilized. Put him on oxygen, now!" He worked frantically with the two nurses assisting him, handing him what he needed before he had a chance to finish asking. After a tense few minutes, he stood up. "Okay, I have him as stable as he's gonna get here. Help me lift him onto the gurney."

Lorne immediately moved to help but McKay stayed where he was, clutching his tablet, his eyes frantically watching the scene unfold in front of him. "Rodney! Get yer bloody arse over here 'n' help!" Beckett snapped. McKay shook himself out of the trance he was in and moved to Beckett's side. "On three. One, two, three!" They lifted John up and placed him gently on the gurney. They rushed back to the transporter. "There's not enough room for all of us in here. You'll have to wait until we get out." He helped position the gurney with its way too still cargo and pushed the locator light closest to the infirmary. The door closed and then opened on the hall just outside the infirmary doors. With the nurse's assistance, he pushed the gurney out and then rushed into the waiting room, McKay and Lorne following them bare seconds later. John was already under the ancient scanner, the nurses cutting away his clothes as Beckett looked on, a worried look on his face as he read the scanner readout.

"What's it showing, doc?" Lorne asked from the position he'd taken up where he could see what was going on but wouldn't be in the way. He reached out and grabbed McKay back to his side as the man started to drift into the working space around the scanner.

"As I expected, he has several broken ribs, one of which punctured his right lung. I need to operate now, he's about as stable as he's gonna get. There's also significant swelling around his spinal cord but it doesn't look like anything is broken, hopefully there will be no paralysis. Not surprisingly, he also has a severe concussion but I don't see any bleeding or swelling of the brain." At the word paralysis, both men sucked in a breath. They knew it would kill John to be grounded. "There's major bruising of his kidneys and liver. There's also a tear in his spleen and he's bleeding internally. I'll have to remove it if I can't repair it, I'll know better once I'm in there. He's in hypovolemic shock from the blood loss." He looked at the two men watching him anxiously. "This is going to take a while. Why don't ye go get something to eat and some rest?" As he'd expected, they both looked at him incredulously. "Okay, I tried. Just…keep out from under foot, will ye?" He motioned to the nurses to come forward. "Prep him for surgery, will ye please?" The lips of one curled up but both did as requested.

When they were out of sight, Lorne turned and asked. "Do you think we should tell Teyla and Ronon, doc?"

"Do ye think either one would care right now?"

Lorne frowned, worried that they wouldn't care or that they might actually do more to harm him; then worried that they'd be furious when they found out that they hadn't been informed. He finally decided to take a chance on their anger and shook his head no. Beckett looked at him sadly and then quickly followed the nurses and his patient into the operating theater. The two men watched them go, consumed with worry. McKay finally turned and said. "Do you really think neither Teyla nor Ronon would care that John's hurt?"

"I just don't know what to think McKay. I never would have thought those two would ever turn against the Colonel. They've always been more like a family unit than a team, you know?"

Quietly, he answered. "I do know Major." Lorne immediately felt remorse, belatedly remembering that McKay was normally a member of that family unit. He put a hand on the scientist's shoulder. "Beckett will fix the Colonel up and then we'll work on whatever plan he came up with to put this all right."

McKay breathed in deeply. "But will it ever be the same again?"

~,~,~,~

Seven hours later, an exhausted Beckett came out of the operating room, pulling off his bloody gloves. He yanked off his surgical head cover and scrubbed his face before looking up. Not unexpectedly, two pairs of eyes watched his every move, anxious for word on their friend. McKay had been there the whole time, working on his tablet to keep busy. Lorne had been in and out as he dealt with the fallout of the Colonel being relieved from duty. He'd yet to tell anyone, including Woolsey, about what had happened, not sure why he felt it necessary to keep it quiet. It was only sheer luck he was with McKay when the doctor came out of surgery.

Beckett sighed, not looking forward to this. He moved to sit exhaustedly next to McKay. Quietly, he said. "It was touch and go. I lost him on the table twice but he's one stubborn lad. I've had to place him on a ventilator and he's in a medically induced coma. The next twenty-four to forty-eight hours are going to be critical. If he can make it through them, he has a fightin' chance. Even if he makes a full recovery, he's facing months of rehab. I'm still not sure about the swelling around his spine, only time will tell on that."

Lorne swallowed hard, trying to imagine the Colonel paralyzed. He had a thought and asked. "Do you think it's safe to leave him unwatched, doc?"

"If ye mean, should ye post a guard on him? Aye, I think it would be a good idea. The people who did this to him, are still out there. Whoever it is though, has to have the gene."

"I'd offer to take first shift but I want to work with you on this plan of yours. McKay, you feel the same?"

"What?" McKay had been staring off into space, turning Beckett's words over in his head, and it took him a moment to register the question. "Oh yes, yes I do. Once we have Kanaan squashed like the bug he is, then I'll take my turn sitting with him."

"Ye know the Colonel hates bugs now, don't ye?"

Rodney looked him right in the eye, fairly vibrating with anger. "I'm very well aware of that fact Carson. It's why I chose that particular phrasing."

"Well…"

Interrupting them, Lorne asked. "What do you think of assigning Stackhouse? He'll protect the Colonel with his life and we can tell anyone who asks, that he's there to make sure the Colonel doesn't escape justice for what he did to Kanaan. That should ease the tensions of those who may still want to punish him."

"Good idea Major. Make the arrangements and then join Rodney and myself in my office, will ye? Also, for now, I think it would be a good idea to keep Colonel Sheppard's injuries quiet. I'll make sure my nurses know as well." He still wasn't happy with their initial reactions to the critically injured man, but both had done their jobs admirably during the surgery.

"I agree doc, I haven't said a word to anyone yet." He reached up to key his comms. "Sgt. Stackhouse, report to me in the infirmary, ASAP."

"On my way Major." Lorne had to smile. Stackhouse was a good soldier, he never asked why, just followed the orders given. He frowned as he realized that was exactly why he liked working under Sheppard. The man encouraged those under him to ask why, to disagree with him until such time as it was necessary to follow his orders without question. Not follow those orders though? That was when you saw a side of Sheppard few ever did and those who did, never wanted to see again. Surprisingly, it worked well. Under normal circumstances most, if not all, of the military on Atlantis would follow their CO anywhere he asked, with no hesitation. He hoped that, should he ever get his own command, he could be the same kind of leader. He just prayed that it wouldn't be today and it wouldn't be command of Atlantis, because that would only mean one thing, John Sheppard was gone and Atlantis would never be the same.

Beckett got up and supervised the nurses who were transferring the gurney holding Sheppard from the operating theater to that section of the infirmary designated as ICU. It was in the quietest corner and closest to the offices where the doctors and nurses sat when not attending patients. When Stackhouse arrived, Lorne filled him in on what had happened and what his orders were. The younger man's face turned purple with anger. "When you find out who did this to him, I want to be part of the detail that takes them down!" He hissed. Belatedly he added. "Sir!"

Lorne put his hand on the man's shoulder. "I figured as much but, listen to me Stackhouse, whoever did this? They aren't really responsible. If what Beckett suspects is true, they've been influenced by Kanaan, their emotions scrambled. Made to feel and do things they normally wouldn't."

"Doesn't matter."

"But it does! Listen, do you remember when Dr. Weir and the Colonel were taken over by Phoebus and Thalen? Dr. Weir shot Ronon and he almost died. She almost made Teyla kill the Colonel. Do you think she should have been punished? Both men forgave her, knowing that it wasn't her that did it, that she had no control over what happened. I think the Colonel would want, and expect, the same for whoever did this."

Stackhouse swallowed his anger and nodded, still not sure how he would react when they found out who hurt the Colonel, but he kept those feelings to himself. He turned to move to the curtained off area that Major Lorne had indicated Sheppard was behind, in critical condition. He couldn't resist peeking in to reassure himself the man was still there. The sight that met his eyes made his stomach drop and his anger ratcheted up. The Colonel was so covered in wires and bandages, hooked up to so many machines, he couldn't even tell it was him. He sent up a silent prayer for the man he would follow anywhere and took up his position outside. Anyone who wanted to get to his CO, would have to kill him first.

~,~,~,~

"So, doc, what's your plan?"

"I think we need to inject Kanaan with another course of the retrovirus. The Wraith DNA that was part of him originally, the 'gift' that he shares with Teyla, may have inhibited the complete transformation back to human. When I did the DNA testing on him, I expected to see some trace of it, so I didn't think twice about what appeared to be small amounts. This is my fault." He slumped into the chair behind him.

Lorne clapped him on the shoulder. "You can't blame yourself, doc. This is all new and uncharted territory. There probably isn't anyone in this galaxy, or ours for that matter, who could have done all that you were able to do. Let's move on."

"Aye. Well, I started to synthesize the retrovirus before we found the Colonel. It's just about ready now."

"Do you have any plans on how to get Kanaan the injection? I highly doubt he'll just offer up his arm!" McKay asked.

"Well, that's gonna be an issue, isn't it? Maybe I can just visit him, pretending Jennifer asked me to do a follow up? Let him think he has me convinced he's badly injured and I just want to give him a shot of pain relief? I doubt he knows that the ATA gene carriers are immune to him."

"You up to that, doc?"

"Yeah Carson, you don't have my acting ability!" Both men stared at McKay. "What? I've told you before, I won a Sears Drama Festival award when I was a kid. I could have made a career out of it!"

Lorne resisted rolling his eyes. "Okay, anyways. Do you think we should go with you, doc? Just in case you have to insist?"

"I'd like the company laddie, but I doubt ye'd be able to get past Teyla and Ronon if they decide to stop us."

"How about this? I just happened to meet up with you as I was heading there to bring them up to speed on the Colonel's removal from command and to tell them I have him under guard. Let them think I'm on their side."

"What about me?" Rodney asked.

"Um, well, I suppose you could just be checking in on a friend?"

"I'd hardly call Kanaan a friend! He has all the personality of a rock, an exceptionally boring rock at that."

"Well then, Rodney, I guess ye'll have to put ye acting skills to work." McKay narrowed his eyes at Carson, not sure if he'd just been insulted or not. A beeping behind them told Beckett that the retrovirus was ready. He got up and loaded a syringe. Moving through the infirmary, he also picked up a syringe of a mild sedative that would have the same approximate effects of a pain killer and added it to his small medical pack, along with bandages and antibacterial creams, all the items one would need to attend to a patient who had just suffered a bad beating. He let his nurses know where he was going and told them to keep an eye on the Colonel. He also told them, in no uncertain terms, to tell no one that the Colonel was there. Unfortunately, he had to add that Stackhouse was there to keep the man in custody to ease their ridiculous fear of the unconscious man. Together with McKay and Lorne, he exited the infirmary and headed towards Teyla and Kanaan's quarters.

~,~,~,~

Teyla looked up from her book when the door chimed. She went to get up but Ronon beat her to it. They were both surprised at the trio standing in the doorway. Beckett smiled at him. "Jennifer asked me tae check in on Kanaan. She was worried aboot him and I told her I'd come tae see him. How is he doing?"

"Hello Carson. He is doing as well as can be expected after what Colonel Sheppard did to him." Teyla stood up to greet them. "Major Lorne, Rodney, what are you doing here?"

Lorne answered as Rodney seemed nonplussed. "I wanted to come by and let you know that Colonel Sheppard had been relieved of duty and placed under arrest. He's being guarded as we speak. Mr. Woolsey has ordered a full investigation and, should the Colonel be found at fault, as he most certainly will, he will be sent back to Earth to face his punishment. I thought you'd like to know that he is no longer a threat to either you or Kanaan." He tried to inject some disgust into his voice when he spoke of his CO.

"Please, come in. That is very kind of you Major and that is certainly good news. I cannot pretend to understand why the colonel did what he did, but he needs to be punished for it. I was somewhat concerned that your military would protect him."

Lorne's stomach cramped as he smiled at her. "No ma'am, we frown heavily on one of our people harming a civilian, or any innocent, for that matter." He looked at Kanaan and forced the smile to remain on his face. "I also wanted to extend my apologies, Kanaan, on behalf of all of Atlantis. What Colonel Sheppard did, in no way reflects on our relationship with you." He held out his hand and the man limply took it.

"No apology is needed from you. It is Colonel Sheppard who is to blame. I only hope, as I heal, that we can put this behind us."

"That's very generous of you." Lorne fought with himself to not wipe his hand on his pants leg when the Athosian let it go.

"Speaking of healing, how about I take a look at ye?" Beckett asked. Kanaan smiled bravely and tried to sit up, focusing on the three men, projecting that he was badly hurt. All three fought to keep the pain from their faces as their headaches worsened. Both Teyla and Ronon rushed to the man's side to help him. Working carefully, the doctor pulled the bandages away from the undamaged skin and made the appropriate appalled noises at the "damage" inflicted on him. "Are ye in much pain laddie? I can't believe what a beating ye took, ye're very brave."

"Some Dr. Beckett, but I try not to complain." The man looked up at him sadly.

"Well, I'm sure that the pain relief that Jennifer gave ye earlier has worn off. I brought some more with me. How about I give ye a top off?"

"That's really not necessary. Teyla has been giving me the tablets Jennifer gave me earlier." Rodney stiffened a little at hearing him use Jenn's given name.

"Ach, those will only put a dent in the pain. Based on how badly I now see ye were beaten, I think ye need somethin' stronger to stay on top of the pain, in order to heal properly. Ye can't pretend it doesn't hurt! How could it not?" Carson was a little afraid he was laying it on too thick, but having seen the way Teyla and Ronon were behaving, he had a feeling this was exactly the way Kanaan expected him to respond.

"If you think it necessary, I bow to your greater medical knowledge Dr. Beckett."

"Carson, please Kanaan."

"Carson." Kanaan smiled, thinking this was going just the way he'd hoped. The bane of his existence was under arrest and disgraced. Teyla was fawning over him as were Sheppard's friends. His life from here on was going to be very good indeed.

Beckett injected the sedative into Kanaan's arm. He gave it a pat and sat back a moment to watch it take effect. When he judged it had, he pulled the second syringe containing the retrovirus out. "This is a combination of vitamins and minerals that should help ye to heal quicker. Are ye okay with that?"

"Of course, Carson." Kanaan's words slurred a little. Injecting the retrovirus in, Beckett sat back and watched, his heart in his throat. He didn't expect any changes immediately, but was unsure how long it would take. The man simply sat there, staring at him.

"Well then, I'll be taking my leave, ye need yer rest. Please, Kanaan, if ye need anything, anything at all, call me." Beckett patted the man's leg, looked up at Teyla and smiled his best physician's smile. She smiled back at him warmly. He stood up to take his leave. Lorne reiterated his apologies on behalf of Atlantis and trailed him out.

Rodney stood there for a moment and then realized he was alone. "I…I…I just wanted to let you know how sorry I am too, Kanaan. This should never have happened. I hope this doesn't mean you'll want to leave Atlantis." He didn't want Teyla and Torren to leave, Kanaan could disappear from the face of the universe for all he cared.

"That is very kind Dr. McKay." Kanaan was still slurring his words. "I know Colonel Sheppard is a friend of yours."

"Yes, well, I'll just be going. I hope you feel better."

McKay practically raced out of the room. Thankfully, both Ronon and Teyla knew he hated to be around sick people and were not suspicious of his rapid retreat. He practically skidded around the bend in the hallway, trying to get away from the man as quickly as possible before he said something that would give them away. He'd desperately wanted to defend Sheppard. Beckett and Lorne were waiting for him.

"Doc, what happens now?" Lorne asked once McKay had caught his breath.

"Now, we wait laddie."

~,~,~,~


	3. Chapter 3

Chapter 3

Carson checked his watch and sighed, exhausted. He'd been on duty for almost twelve hours, seven of them spent trying to keep his friend alive. John had been out of surgery for just over three hours and was stable so far, although he was worried about how low the man's blood pressure was from the loss of blood. He was on fluids now to help alleviate that, but would need to be closely monitored. Luckily, it has been a slow night other than the emergency surgery. It had been just a little under two hours since he'd administered the retrovirus to Kanaan. He'd heard nothing that would indicate that it had started to work. He wasn't even sure if it would work with just one application, he might have to administer a second round. He rubbed his forehead, the ever present headache still there. He wasn't sure if it was still because of the effects of what Kanaan was doing or if it was just stress. Jennifer was due on duty at ten hundred hours, just ten minutes from now, and he still wasn't sure how she was going to react to what had happened to the colonel. He knew she'd been instrumental in getting the man removed from duty.

He brought up the scan of Kanaan once again, staring at it and wondering what she'd seen. He heard movement behind and knew Jennifer had arrived. He made a decision and expanded the scan a little, hiding the patient's information. He turned when she entered the room. "Ye're early, love."

Jennifer smiled at him. "Just a few minutes Carson. Anything I should know about?"

There was a lot she needed to know but for now he just went with his hastily formed plan. "Actually, I could use yer help on this. I have a headache and it's making it hard to focus." He indicated the scan on the screen. "Can ye take a look and tell me what ye see?"

Jennifer moved to stand behind him, looking at the screen over his shoulder. She frowned. "It's a perfectly healthy male. What did you expect me to see?"

Carson collapsed the screen so she could see whose it was. Her eyes widened as she took in the information that this was the scan from yesterday. "This isn't his scan! I know John is your friend Carson but why would you alter Kanaan's medical records?"

He stared at her, open mouthed and felt rage wash over him at her words. "I can't believe ye'd accuse me of such a thing, _Dr_. Keller. Even if I knew how to manipulate the ancient technology, I would never do something like that!"

"I'm sorry, I'm sorry! I don't know why I said that, I know you wouldn't. It must have been Sheppard! He's been around Rodney long enough to pick up the knowledge of how to do something like this! He's trying to destroy the evidence that could get him court martialed and possibly jailed!"

" _Colonel_ Sheppard would never do something like that!"

"Wouldn't he? He savagely beat a man just yesterday!"

Carson rose and grabbed her arm. Pulling her along with him, he left the office and marched towards the ICU area. She was so surprised at his actions, she let him drag her with him. She immediately noticed the armed man standing in front of the privacy screen. "What's Sgt. Stackhouse doing here and why is he armed in the infirmary?"

Carson dropped her arm and moved the screen aside. "Ye want to see someone who was savagely beaten? Take a good look!" She looked at the bruised face of the man she had just accused of hurting another, noting the ventilator, the bags of fluid and his complete stillness. "It took me seven hours to fix what was done to him and I almost didn't succeed! I'm still not sure he'll survive this. Sgt. Stackhouse is here to protect the Colonel from the people who did this. As ye can see, he's in no condition to be hacking into the ancient's medical database and changing patient records!" Behind him, he could hear Stackhouse suck in a breath and he motioned him to stay quiet. The look on the man's face said it all. He desperately wanted to defend his CO but Carson needed Jennifer to stay focused.

She stared at the man in the bed and then the doctor in her took over as she walked to his side to check his vitals. Reading the monitors, she could see that his blood pressure was dangerously low. She turned to Carson. "How? Who?"

He felt the anger drain away, leaving him more exhausted. To have her suggest he would do something so unethical, had hurt him deeply as he liked and respected the young doctor. She'd worked tirelessly to help him when his cloned body had begun to breakdown without Michael's drugs, never giving up on him, so her words had slammed into him, even though he knew she wasn't really herself.

He sighed. "We don't know, lass. All we do know is that everyone on the base who doesn't have the ATA gene, now appears to harbor a deep seated dislike and mistrust of the colonel. Those of us with the gene, are experiencing headaches but not the change in how we feel about him. Don't ye see? Kanaan is doing this. We think that he retained some of the Wraith abilities from what Michael did to him. Don't ye think it odd that ye went from considering John a good friend to disliking him enough to get him relieved of duty?"

"You didn't see Kanaan when he came in Carson! He was badly beaten and bruised, with cracked ribs. Ronon saw the whole thing!"

"Ronon saw John beating Kanaan that badly and didn't step in to stop it? He just let it happen?" Jennifer's mouth opened and closed a couple times, not able to come up with a response. "I went to visit Kanaan a couple of hours ago. What I saw was a perfectly healthy Athosian, with no signs of having taken a beating. Both Teyla and Ronon, however, were still seeing what ye saw. Major Lorne and Rodney went with me. Neither of them saw bruises and both are suffering from the same headache as meself and the sergeant here." Stackhouse nodded his head vigorously, wincing as he did so. "I played along and tutted over the bruises, Lorne even went so far as to apologize on behalf of all Atlantis personnel. Kanaan just drank it all in, acting like he could barely move from the pain but was putting on a brave face! When Lorne told them that John had been relieved of duty, they were all pleased, Teyla especially so. It all made me ill!"

"Why would he do this?" She asked quietly.

"We're aren't sure, but we think he wants to remove John from Teyla and Torren's lives. It makes the most sense. What better way than to get him accused of attacking a civilian? It would most likely result in John being forced to leave Atlantis and Teyla, as well as Ronon, would no longer see John as the good friend he is. Ye know that the two of them are in denial about how they feel about each other but anyone with half a brain can see the love between them. I'm sure Kanaan has seen it and it can't be a good feeling to know the woman ye're in a relationship with, the mother of yer child, is head over heels in love with another man!"

"I…I don't know what to say! I still feel a great dislike of him and, even in his condition, I'm afraid of him." She looked like she wanted to cry as she thought over his words. She remembered liking the Colonel immensely, feeling like he was good for Rodney, forcing him out of his lab to participate in the real world. She knew she herself wouldn't be alive without him. He'd risked his life and been impaled by a tentacle of the creature she'd been turning into after he'd managed to get her the medicine she needed to stop the transformation and start reversing it. He'd never blamed her. He'd saved all their lives on more than one occasion. He wasn't without his faults, but she'd always felt safe knowing he was around, knowing that he'd do anything to protect the people on Atlantis and even those that they met along the way. How could she have forgotten all that?

"I understand Jennifer, but _ye_ have to understand, it's not a natural fear, it's being imposed on ye."

"What can we do?" She whispered.

"I've given Kanaan more of the retrovirus. Right now, all we can do is wait until it takes effect, if it does. If it doesn't, we'll have to come up with another solution, I just don't know what it would be. One other thing, we've not notified anyone that John was hurt. The only ones who know are me, Lorne, Rodney, Stackhouse, the two night nurses, Sheila and Paul, and now you. Oh, and the people who put him here! We'd like to keep it that way as long as possible. We're not sure if someone else might be influenced to come in and finish the job while he can't defend himself." She nodded at his words and opened her mouth to ask more questions, but couldn't put words to them.

His shift was up and Carson went to leave but then turned back. He patted Jennifer on the shoulder and tried to smile. She made the same attempt, but neither one was successful. She watched as he left the infirmary and turned back to the man in the bed. She made herself reach out and touch him gently. Yup, the dislike and fear were still there, making her feel like she wanted to snatch her hand away and run from him. Carson was right, this wasn't natural. She patted his arm and went into the office she shared with the other doctor, her heart heavy as were her footsteps.

~,~,~,~

Two days passed without things changing. Carson made another visit to Kanaan and gave him another course of treatment, under the guise of medicine to help him heal. He was starting to worry that the retrovirus wasn't going to work. They'd been able to keep John's presence in the infirmary a secret. Lorne had told anyone who asked, that he was in the holding cells, waiting for a decision on what was going to be done with him. It had been a quiet few days and the few people who had wandered in for something, were kept far from that area of the infirmary. The tired doctor was once again handing the reigns over to Jennifer, who still couldn't shake her feelings for John, although she was professional and took good care of him, when both their comms activated.

"Carson? Jennifer? It's Teyla, can you come to our quarters? There's something wrong with Kanaan!" Teyla sounded frantic.

Jennifer met his eyes and swallowed hard. "You go Carson, I'll stay here and keep watch over…John." She still hesitated before using his given name, the dislike and fear still active even as she was trying to override it with the logic of what he'd told her.

"Thanks lass." He keyed his comms to direct his next words only to one person. "Major Lorne?"

"Lorne here doc, anything yet?" Lorne sounded as tired as he was. The transition of command from the Colonel to him had not been an easy one. Those with the ATA gene were still loyal to their military commander, adamant that he'd never do what he was being accused of. Those without it were just as adamant that he had and that he was a threat to all of them. The major had been running around breaking up fights since.

"Not sure laddie, but I just got a frantic call from Teyla that something's wrong with Kanaan and she's asked me to come to their quarters. I'm heading there now, would ye like to join me? And can ye get Rodney?"

"Absolutely. I'll find him and we'll meet you there. Hopefully, this is it!"

"Aye, hopefully."

~,~,~,~

Once again it was Ronon who opened the door at Carson's knock, he hadn't been far from Kanaan's side since the beating. He stood back to let them enter and Carson moved to Kanaan's side. He was rocking in place, his eyes tightly closed, holding his head as Teyla tried to soothe him. Suddenly, his eyes opened wide and he stared at the doctor. "What have you done?" He screeched. He pushed Beckett away and stood up, frantically trying to reach out to Teyla with his mind. Even his original gift was gone! Teyla swayed on her feet, his influence over her waning. Lorne stepped forward to grab her before she fell, easing her back onto her chair. Ronon staggered and fell against the wall, his eyes blinking furiously. Rodney and Beckett kept an eye on Kanaan, worried about how he might react, Rodney's hand trying to stray to the butt of the gun he wasn't wearing. The man just stood there, his mouth opening and closing but no words coming out.

The Major cautiously approached him. "Kanaan?"

"It is gone! It is all gone! You have left me with nothing!" With that, he lunged at Carson only to be hit by a red bolt from Ronon's gun. He dropped to the floor.

"Ronon?" Teyla asked.

"Don't worry, it was set to stun. I should have killed him for what he's done to us, but I know Sheppard wouldn't want it that way. And I know he's still Torren's father."

"John!" Teyla gasped. "I need to see him!"

Ronon nodded. "We both do. Lorne, Sheppard didn't hurt Kanaan. Somehow he made us believe that he had. You need to release him from custody and put him back in charge of Atlantis."

Lorne wasn't sure how to tell them. Slowly, he said. "Well, we obviously knew something was wrong. Whatever influence Kanaan had over people, it didn't work on those of us with the ATA gene. It only gave us a headache." He realized the pressure in his head was gone. He took a deep breath. "Colonel Sheppard is not under arrest but he is being guarded, for his own safety."

"Can you take us to him? I need to talk to him. I need to apologize for ever believing he would deliberately beat an innocent man." Teyla requested, Ronon now standing by her side, watching Lorne carefully.

When he didn't answer right away, Ronon asked. "What happened? Where's Sheppard?" The man might look like all brawn and no brain, but he didn't evade the Wraith for seven years without being smart and observant. He knew something was wrong and he knew it had to do with his friend.

Beckett was the one who answered. "Someone attacked the colonel and beat him pretty badly. He's in the infirmary."

Ronon and Teyla both looked at him in horror. As one, they headed for the door, Teyla stepping over Kanaan's inert body as if it were not there. Rodney stepped in front of them, stopping them from leaving, his face lined with pain. Beckett came up behind them and softly said. "Ye can't see him just yet. He's in critical condition. He barely made it through surgery and he crashed last night. We had a hard time bringing him back."

Tears tracked down Teyla's face without her even noticing. "All the more reason that we need to see him. Please Carson, I need to be with him!"

Lorne lost track of the conversation when his comms activated. "Captain Jennings to Major Lorne, please respond."

"I'm here Jennings but I'm a little busy right now. What's the matter?"

"I just wanted to let you know that Manning, Johnson, Delaney and myself will be turning ourselves over for disciplinary action. We're on our way to the holding cells as we speak."

He had a feeling he knew why but he wanted to hear it. "For what reasons, Captain Jennings?"

"The four of us beat Colonel Sheppard to death and…and…just left him on the East Pier. You need to send someone out there to retrieve the body. We have no excuse and no idea why we did what we did, but we need to be held accountable."

"The Colonel isn't dead Jennings, he's in the infirmary. Dr. McKay and I found him and got him to Dr. Beckett. He's not out of the woods but he has a fighting chance."

The sigh of relief was heartfelt. "We'll still be reporting for discipline, we beat our CO to a pulp, there's no excuse."

"Go ahead and report, but I have a feeling the Colonel will have something to say about this when he's awake. You were under the influence of someone else and not responsible for your actions."

"I find that hard to believe."

"Believe it. I'll be down shortly to talk to you. Lorne out."

He realized everyone was watching him. "The four men who beat up the colonel, just confessed and are turning themselves in, placing themselves in the holding cells."

Beckett frowned. "We heard what ye said and I agree laddie, those men had no control over their actions, they were influenced by Kanaan."

"Doesn't stop the guilt, doc."

"Aye, well, we'll have to work on that."

"Doctor Beckett? How was Kanaan able to do this?" Teyla looked down at the man she had shared her bed with, who she shared a child with and felt nothing but revulsion. How long had he been controlling her?

"I think we stopped the retrovirus treatments too soon and left him with some Wraith like powers. Powers that he used to influence those around him. Based on the results from giving him another round of treatment, it would appear I was correct. He should be harmless now but I'll do a thorough work up before I make that mistake again."

"Why would he turn people against Sheppard though? He saved Kanaan's life, saved Teyla and their child, got them off that hive ship and gave him a home here on Atlantis. It doesn't make sense." Ronon said.

Beckett looked closely at Teyla and saw when the reason hit her. She raised a hand to her lips and pressed hard, keeping the cries inside. "Teyla understands. Ye see, Kanaan saw what the rest of us have seen for years. The love she and John have for each other may never have been spoken or acted on, but it's there, obvious to everyone but them. He saw John as a threat to his relationship with her and we believe this was his effort to remove a rival for her affections."

"John has feelings for me?" Teyla watched Carson carefully, wanting to believe what she heard, but worried that it was just the romantic Scotsman's imagination. Her first thought had been that Kanaan had done this because of her feelings for John, not because John felt the same way for her.

"Aye, lassie. How could ye not see it?"

"I…I guess whenever something happened to make me think he did, I put it down to wishful thinking. He never let on, never said a word to me!"

"Yeah, well, that's Sheppard for you! Not one to talk about how he's feeling!" Rodney himself wasn't sure about this whole Teyla loves John, John loves Teyla thing. How could he have missed it? Not that he'd ever admit it.

"McKay!" Lorne stepped in. "Look, Teyla, I think he was afraid you didn't feel the same way. Afraid if he said something and embarrassed you, it would ruin your friendship and I know he values that very highly."

She nodded a little and looked over at Beckett again. "Please Carson, if I am very quiet and do not make any trouble, could I see him? Even if just for a few minutes?"

"Aye, lassie, I think it might be good for him. I imagine he's felt mighty lonely the last few days." Both Teyla and Ronon looked ashamed at his words. "No! I didn't mean it as a rebuke for ye two! Ye were both under the same influence as those four men who beat the colonel, the same as Dr. Keller who saw bruises and fractured bones where none existed. I had to practically force my nurses to help me work on him during surgery, I think they wanted to just leave him to die. It was none of yer faults!"

Teyla put her hand on his arm. "Thank you Carson. Could we go now?"

"Of course." He looked down at Kanaan. "Major, what are we going to do with him?"

"I'm not sure, doc. I think I'll let Mr. Woolsey handle that one. For the moment, I think I'll put him in a holding cell. Ronon, want to help me get him down there before he wakes up?"

Ronon snarled. "With pleasure." Bending over, he yanked Kanaan up and hoisted him over his shoulder with no ceremony and little concern for the man's wellbeing.

Lorne's eyebrows went up. "Okay then. Shall we?" The two left the room. Teyla watched them go forlornly.

"Teyla, love? What's going on in that pretty head of yers? Ye know ye can talk to me."

"I find myself wondering when it all went wrong. I have loved John from the moment he, Aiden and Colonel Sumner walked into our camp. I suppressed it, I was the leader of our people and he was an off worlder and yet, after he brought my people to Atlantis to save their lives, I let him talk me into being a member of his team, always in close contact. Not exactly the best way to stop my growing feelings. At some point I realized I would follow him anywhere but he never showed anything other than friendship for me. Kanaan's attention flattered me. He was someone I have known all my life and who I used to be attracted to. I will never regret it, as it brought me Torren, but how much of it was my decision and how much was his influence over me?"

"Teyla, before Michael, he had no power over ye. What ye did, ye did of yer own free will. It wasn't until he was rescued and given the retrovirus, that he must have discovered his new found powers and decided to use them for his own nefarious plans. Now, what say we head down to the infirmary?"

Teyla nodded and went over to Torren's crib. Surprisingly, he had slept through it all. She picked him up and looked at the doctor. "I cannot leave him here alone."

"That's fine lassie. As long as he remains quiet, he can stay with ye. If he gets fussy, Jennifer can take him into her office." All he wanted right now, was his bed and maybe a wee dram of whiskey.

"Thank you Carson, for everything."

"Ye're welcome love."

~,~,~,~

Teyla sat at John's bedside, Ronon at the foot, his boots propped up on the bed, and Rodney sat on the other side, tapping away on his tablet. It was all very familiar. She reached out and pushed a lock of his hair off his forehead. When she'd seen him that first day, she had been so sure he was already dead. Covered in bandages and attached to so many machines, one of them breathing for him, she'd caught her breath. Sgt. Stackhouse had been waiting, taking his turn guarding his CO and had walked up behind her, putting his hand on her shoulder to give comfort. "I know how you feel ma'am. I couldn't believe it when I first saw him either. But the Colonel's strong and he's stubborn. He'll make it through this, you just watch!"

She'd thanked him and he'd left, no longer needed to keep the Colonel safe now that Kanaan's influence was gone, leaving her to sit by the bed, Torren asleep in her arms, to watch the rise and fall of his chest in time with the woosh, woosh of the ventilator. She'd reached out and taken his hand, stunned at how cold it was. John was always warm, always vibrant, always larger than life. That quirky crooked smile and the light of mischief in his eyes had drawn her in from the first. It felt so wrong to see him this way. She'd leaned over and gently kissed his hand. Moving up, she'd pressed her forehead to his in the traditional Athosian greeting. She'd whispered to him. "You need to come back, John. We need you here. I need you!" She drew in a deep breath and moved her lips to his ear. She'd breathed out. "I love you Lt. Colonel John Sheppard."

That had been just over three weeks ago. He'd been weaned off the ventilator at the beginning of the second week as his lung had healed enough to no longer need it and he continued to improve, but he was still in a coma. She knew Carson was concerned, he'd done test after test and couldn't find anything else wrong, even the swelling along his spine was all but gone, both Jennifer and Carson agreeing that there would be no paralysis. People came and went, wanting to see him, trying to make sense of the feelings that had been forced on them, only to disappear abruptly when Kanaan's powers were taken away, leaving them dizzy and nauseated.

The four marines who had beaten him were exonerated but showed up daily to sit with the man they all liked and admired. She knew it would be a long time before they would be able to forgive themselves, but she'd let them know that she did, knowing that that was what John would want. Mr. Woolsey had immediately reinstated him as commander of Atlantis but was now worried he'd have to bring in a new commander anyway, if the Colonel didn't wake up soon. They all knew who that would be and, while Colonel Caldwell had mellowed over time, the whole base was uneasy with the thought.

John was being fed through the machines, but he'd still lost weight he could ill afford to lose. One of the physical therapists came daily to work on his muscle tone, so that they didn't atrophy from disuse. The three of them watched carefully until the therapist had allowed them to help. From then on, they'd done the exercises for their friend, under the watchful eyes of whichever therapist was on duty.

Kanaan was sent back to the mainland, Woolsey not sure what to do with him. Halling had been informed of his actions and had agreed to take him in, not wanting Torren's father to be banished. He barely spoke to anyone and kept to himself. He pulled his weight in the village and they soon became used to his quiet presence. If Halling was concerned about what would happen when Teyla or Colonel Sheppard next visited, he kept it to himself. The Atlantean's ways were often confusing to him but he had a great respect for the Colonel. He knew his own son, Jinto, adored the man and he seemed to return the boy's affection. He'd gone to the city of the ancestors to pay his respects shortly after the incident and was stunned at the damage that had been done. Never had he seen anyone beaten so badly and live. They truly had amazing healers. He waited daily to hear that the man he considered a friend had awoken, saddened when each day passed without the welcome news. He offered up his prayers to the ancestors for his recovery, as he knew many of his people did.

The city itself seemed to be waiting for him to wake up. Daily, more glitches were reported, power surges and outages happened for no apparent reason and kept Rodney and Radek racing around. Three people had been trapped in a transporter for six hours when it had simply stopped working after they'd stepped in, refusing to take them to their destination or to let them out. Rodney had finally overridden the door controls and they'd made their escape. Not one of them would get in a transporter again and, instead, walked everywhere, claiming the exercise was good for them.

Ronon rarely left John's side, his own anger at himself for siding with Kanaan over John, barely dented by the reality that he'd had no control over his actions. Rodney was surprisingly quiet, worn down by putting out fires every time he turned around. Jennifer had snuck in one night to softly apologize for her treatment of him when he'd come for his aspirin. Teyla had just returned from the cafeteria and stood in the shadows as the young doctor tearfully voiced her heartfelt apology. She never mentioned what she'd overheard, that was between John and Jennifer.

Torren didn't seem to miss his father. He surprised Teyla by always remaining quiet when they sat by John's side. The first time the baby reached out a chubby hand to touch John, she'd kept close watch on him, worried that he'd dislodge something important. Instead, he'd just gently patted the arm closest to him and left his hand there. He seemed to know John was asleep and quiet was needed.

Carson came in and stood behind Teyla's chair. "Will he ever wake up Carson?"

"Ah, love, I wish I could answer that. There's no apparent medical reason why he shouldn't be out of it by now. I wonder…" He stopped.

She turned and looked up at him. "You wonder what, Carson?"

He sighed, wishing he hadn't started that particular train of thought, knowing she wouldn't let it go now. "I wonder if maybe he just doesn't want to." He replied softly.

"You think we hurt him that badly?"

"I think he's feeling safer where he is right now." He replied sadly. He patted her on the shoulder and left to do his rounds. While the colonel was always on his mind, he did have other patients to attend to.

John floated in darkness, feeling no pain, emotional or physical, and had no desire to change a thing. Here, there was no one accusing him of things he hadn't done, no one taking away the only things that made his life worth living, the woman he loved more than life wasn't looking at him like he was a monster. He idly wondered if that made him a coward and decided he didn't care. A soft light broke the darkness and he tried to turn away.

"John." The voice was melodic and floated on the air like butterflies. Wait, that didn't even make sense. He ignored her. "John." The voice spoke again.

He sighed. "What do you want? Who are you?"

"You know me as Atlantis."

He laughed. Now he was going crazy. "No, John, you are not crazy. You know who I am. You have felt me in the back of your mind, seen me in the corner of your eye, since the day you stepped through the gate. We have been connected since that moment. You need to wake up now. Your friends need you. I need you awake and walking my halls, protecting me like you do the ones you love."

"They don't need me. They all turned on me, I have nothing left to go back to."

"You are wrong, John. They are all here, waiting for you to wake up. What happened was not their fault. The one known to you as Kanaan, had the ability to influence their thoughts and feelings. He used that to turn them against you. He has been neutralized now. It is time for you to go back."

"How was he able to do that?" He ignored her request to go back.

"He had the abilities of the Wraith to control those around him. Your Dr. Beckett figured things out and was able to stop him. It is not your time to leave this world, but if you do not go back, your body will eventually fail. Your leader is already worried that he will have to replace you, something he does not want to do. Can you not find it in your heart to forgive them for what they could not control?"

"Of course I can."

"Then why do you not?"

He had no answer to that. He turned to look towards the light. Gradually a female form coalesced. He started, the face was that of his mother. "I take this form from your heart and your memories. I was not given a corporeal representation by my makers. I appear to those that I connect with in a form that mimics someone they had great love for, someone who had a great influence on their lives. For you, that is your mother. It is meant as a showing of great respect."

He stared at her, the planes of her face as familiar to him as his own, even though she'd been gone most of his life now. He'd always been told he took after his mom and not his dad. That was Dave, in more ways than one. With an adult's perspective, he could see the resemblance now. He reached out and touched her, surprised to find a physical form. He ran his hand down her cheek and she turned into his palm. "Of all the ones I have connected with over the years, you have become my favorite. Your bravery and loyalty exceed all that have gone before. Your need to hide your feelings, however, does not serve you well. There is one who waits for you with love in her heart, love that has been there since the beginning. Your inability to express your feelings for her, led her to another. The child they created together is exceptional and needs your guidance. His father has been removed from his life and will not be a negative influence. However, without you, he will not reach his full potential. You must go back John."

"So you have the ability to see the future?"

She sighed, he was not going to make this easy for her. Then she had to smile, his stubbornness was part of what she loved about him. "See the future, no. I was built to be able to process large amounts of data at one time. I can follow trails to their natural conclusions. Torren's trail will end differently without your loving presence in his life. Do you really want to stay here, in limbo, until your body finally gives up?"

"No. No, I don't. I'll go back." He paused. Speaking softly, he asked. "Will I see you again?"

"If you want to, yes. Much depends on your willingness to suspend your disbelief. You are in a state of mind right now that leaves you more open to me. If you can take that back with you, I will see you again."

"I'd like that."

"As would I. Now, it is time to go." She faded away but the light didn't diminish. He opened his eyes to find himself staring at the ceiling of the Atlantis infirmary. He turned his head slightly to find Teyla sitting by his side, her eyes closed, Torren in her arms, his small hand resting on his wrist. He slowly, and with much effort, turned his hand up to grasp the small one in his. The boy's eyes opened and he grinned at him gummily. Was that a tooth? He gurgled something that sounded like it could, with a lot of imagination, be "John" and Teyla started awake, her first instinct to shush the child. When she followed her son's gaze to the man in the bed, finding his eyes open and watching her, she began to cry.

"Hey Teyla, you okay?"

~,~,~, ~

A/N – I loved this show and would love to see Joe Flanigan get his hands on it and resurrect it, although that seems like a pipe dream now. I recently rediscovered it and fell in love all over again. When it dropped off Amazon Prime as free, I frantically checked all other venues and found it on Hulu, to which I promptly subscribed.

A/N2 - Thanks, as always, to honus47 for being my beta. All mistakes left are mine!


	4. Chapter 4

A/N – This was originally completed with chapter 3 but I had several people tell me that it felt incomplete, that the ending was too abrupt. Considering that this started out as a one shot that somehow morphed into a multi chapter story, I figured, why not? So, here's a new ending, hope you like it! Feel free to let me know what you think…wink…wink.

~,~,~,~

Epilogue

The sound of his raspy voice caused Ronon to drop his feet from the bed, practically exploding from the chair he'd been dozing in. On the other side, McKay also jumped to his feet, his precious laptop hitting the floor unheeded as he shouted. "You're awake! You're finally awake! I need to go get Carson!" With this pronouncement, he scurried from the room.

Sheppard's eyebrows shot up at the commotion and he looked at Ronon who only stared back at him, his face a blank mask. John frowned at him and watched as his friend stiffened and then turned way, starting to leave. "Ronon?" When there was no response, he tried to raise his voice but found it much weaker than he would've liked. "Ronon!" The man stopped but didn't turn around. "What's going on?"

Facing away from him, the Satedan responded. "I know you don't want me here. I'm just glad you're finally awake."

"Why wouldn't I want you here?" He had a feeling he knew why.

Ronon turned, a look of disbelief on his face. "Why would you? I turned on my Commanding Officer. Not only that, I turned on my friend. I sided with Kanaan against you."

John remembered Atlantis's words. "You had no choice, buddy. Kanaan had control over you." He looked at Teyla who had yet to say anything, tears still running down her face, Torren on her hip gurgling at him, the only one who seemed calm at the moment. "Over all of you! None of this was your fault. Any of you!"

"I should have been stronger! I've been forced to be a Wraith worshipper, under their control! I know what it feels like! I should've known something was going on, I should've known that you'd never do what he accused you of, yet it never entered my mind to believe _you_ instead of _him_." The last words were said with self-disgust.

"And that's on Kanaan, not you! I know you'd never turn on me willingly! You've saved my ass too many times over the years. I know you, you're one of the most honorable men I've ever met." Ronon hmphed and folded his arms across his chest, unwilling to let the man he thought of as a brother, a man he'd let down so badly, let him off the hook that easily. "Look, I've been there! When that damn retrovirus started turning me into a bug, when Thalen took me over and tried to use me to kill Elizabeth, when the crystalline entity came back to Atlantis with me after I stupidly touched it, don't you think I had regrets about the things I did while under their control? Regrets I still have? Don't you think I worried that no one would ever be able to trust me again? But you did, you all did. How could I do any less?" His speech tired him more than he wanted to admit.

Ronon blinked as he processed his friend's words. He dropped his arms to his side and tilted his head to the left. John waited while he thought. When a slight smile appeared, he knew it would eventually be okay, even if it took some time, they were on the right track now. He might have some moments of bitterness in the future, but Atlantis had been right, his friends, his _family_ , were not to blame and they were worth it. He turned his attention to Teyla, who had yet to say a word. "Teyla?" His voice cracked and she quickly moved to the table by his side, picking up a cup of water with a straw in it. She wordlessly held it to his lips and it dawned on him just how thirsty he was. He sucked greedily at the water, frustrated when she took it away too soon. He tried to lift his hands to pull it back and barely managed to get them more than an inch of so off the bed. He frowned and she leaned forward to brush a hand gently down the side of his face.

"You cannot have too much too soon, John. You need to wait for Carson."

"Why?" He hated how whiny he sounded.

"Ye've been ill for quite a while, laddie! I need to check ye out before I allow any more." Carson had returned with Rodney without John noticing it, his attention focused on his team mates.

"How long is quite a while, Carson?"

"A little over three weeks."

"Three _weeks_!" To say John was stunned, would be an understatement. "Why so long? What was wrong with me?"

Beckett cleared his throat. "Ye were beaten severely and almost died several times. I had to fight to keep ye here with us. Yer body needed time to heal." John watched him, knowing he was holding something back.

"And?"

"And what?"

"What aren't you telling me doc?"

Teyla spoke. "Carson believes you did not want to come back John. That you did not want to come home to us." Her voice broke a little.

He was silent for a moment, knowing that the doctor was right. He hadn't wanted to come back until Atlantis had made him see it was wrong. He tried to reach out to her and she instantly took his hand in hers. "That might be true, but someone very smart made me see how wrong that was. I belong here, with you." He turned and looked at them all. "With all of you."

The relief in the room was palpable as they all started to talk at once. Carson raised his voice a little. "All of ye, out now. I need to check John over. Ye can come back later. I think it would be a good idea if ye finally got something substantial to eat and some rest. Now shoo!" Each reached out to touch him as they said their goodbyes, almost as if they needed to be reassured he was really there. When it was just the two of them, he went into full doctor mode, taking John's vitals, checking his blood pressure and, when he was satisfied that all was well, raised the back of the bed so his patient could sit up a little. "Ye'll need to take it easy for a while John, yer body underwent a severe trauma and ye haven't moved around much in weeks. Ye'll be weak and, knowing ye, very frustrated, but ye must take yer time!" He helped John drink some more water until he'd finally had his fill.

John thought of something. "Carson, why was Rodney unaffected?"

"We think it was the ATA gene. Neither Rodney, Lorne, Sgt. Stackhouse nor meself, among others, were affected, other than a bad headache."

"How did you reverse it?"

"How do ye know it was me?"

"First, you're one of the best doctors I've ever known, if anyone could figure out how to deal with it, it would have been you."

Carson waited. When the room was quiet for a few moments, nothing more forthcoming from the colonel, he prompted. "First?"

John swallowed. He still wasn't sure if he wanted to share what had happened in the last moments of his unconsciousness, worried that they'd think he was brain damaged.

"Colonel?" Carson tilted his head at him.

"Fine, someone told me." If John had been able to move, he would have now been the one folding his arms over his chest.

"Someone? Ah, Ronon, Teyla or Rodney?"

"Um, no." He knew Carson, knew he wouldn't let it go and would ask each of them if they'd been the one to inform him of what had happened.

"Then who?"

"I don't know if you'll believe me if I tell you."

"Why don't ye try me? I've seen things in this galaxy that I'd never thought would be possible." He paused. "John, I'm yer friend as well as yer doctor. Ye can tell me anything."

"Fine, Atlantis told me." He waited for the doctor's response. When it came, he knew he shouldn't have been surprised.

"Was she also the one who told ye it was wrong to stay hidden away from us?"

John blinked a couple times. "Yeah, it was and I never said Atlantis was a she."

"Ye didn't have too. Ye're not the only one with the ATA gene. I've always suspected that the city had its own consciousness and I've always thought of her as female. It was just a feeling that she was alive and happy to have us here with her."

"Really? Why didn't you ever say anything?"

"Well, it's a wee bit of a stretch, don't ye think? Wouldn't do to have people thinking the doctor was barmy, now would it?"

John looked him in the eye and then smiled, Carson joining him. It felt good to be back.

~,~,~,~

The next day, Carson stood at his side again. Even though he'd been unconscious for more than three weeks, John felt tired all the time and had fallen asleep shortly after his conversation with his team mates and the subsequent one with the doctor. He'd slept all night, this time a natural and healing sleep, and had only just awoken again. "Colonel, do ye feel up to some more visitors?"

John yawned and blinked as he nodded. Carson raised the back of the bed again and left. He heard voices outside the privacy curtain and then it moved aside to let Richard Woolsey and Evan Lorne in. His gut clenched as he remembered being relieved of duty. While it seemed that everything was back to normal, he still wasn't sure how to deal with the expedition leader. "Mr. Woolsey." He said guardedly.

Woolsey winced and sighed. Taking off his glasses, he polished them nervously on his uniform. Putting them back on his face, he met Sheppard's eyes. "Richard please, Colonel. I'm here to tell you how sorry I am about what happened. I can't imagine anyone else in command of Atlantis's military and I hope you can find it in your heart to forgive me. You were fully reinstated as soon as the retrovirus released us from Kanaan's control. I've brought the SGC up to speed on what happened and they backed me one hundred percent."

John had to chuckle. "Bet Caldwell was pretty frustrated by that! He's come so close, so many times, to finally getting to be the CO of this base."

"Perhaps, but I will tell you that Colonel Caldwell was the first to say that reinstating you was the right thing to do."

"He did, did he?"

"Yes. Look, Colonel…"

"Richard, I thought we were past that. You used to call me John." With that, he let Woolsey know that he'd accepted the man's earlier apology.

"John." For the first time in weeks, Richard felt a weight lift off his shoulders. "I really am sorry. I've always prided myself on being a logical man, but what happened, what I did, was NOT logical."

"And not your fault." John turned to Lorne, indicating that that line of conversation was over and behind them. "How'd you like being in charge, Major?"

"Relieved you're awake and can take it back sir! I believe I like being 2IC better. Mr. Woolsey actually threatened me with having to do evaluations!"

John chuckled, understanding exactly what Lorne had been feeling. "I guess that means they're not done and I'm still stuck with them?"

Lorne grinned from ear to ear. "Yes sir!"

The two men smiled at each other and then John's curiosity kicked in. "Richard, what happened to Kanaan?"

The man sighed again, not sure how the colonel would take the news. "We didn't quite know what to do with him, to tell the truth. He was not under my command or yours so, technically, wasn't subject to our discipline even though he lived here on Atlantis. There's nothing in the regulations about how to deal with someone who used mind control to influence other people and force them to attack another. I brought in Halling, who is very happy to hear that you're awake, by the way, and told me to tell you Jinto sends his well wishes. They would both like to visit when you're feeling up to it."

Realizing he'd gotten off track, he continued. "Anyway, Halling agreed to take Kanaan back to New Athos and deal with him as an Athosian. He could have been banished, but the council felt that there were mitigating circumstances after having been used against his will by Michael. The man who did this was not the man they used to know. In addition, he is Torren's father and they didn't want to have the child grow up with that stigma. From what I've been told, Kanaan is being a model citizen, doing his work and keeping to himself. He hasn't expressed any remorse over his actions, but then he hasn't spoken much since Ronon knocked him out with his blaster."

"Ronon shot him?"

"Yes, apparently he went after Dr. Beckett when he realized he'd lost all his powers, including the one he was born with, the one he shared with Teyla."

John thought about it. "That's gotta be tough, to lose something that has been a part of you your whole life."

"I would imagine, but he brought it on himself."

"Did he? Or did we bring it on? Without us, there would've been no Michael. The Athosians would still be whole, never would've suffered at his hands. Teyla would never have had to kill Michael to protect Torren from him."

Woolsey nodded, knowing that many of the expedition members still felt guilt over what had happened. The old expression, the road to hell is paved with good intentions, passed through his mind. Straightening his shoulders, he said. "Well, now that we've cleared the air, I have a lot of work to do. I'll leave you two to talk." He reached out to shake John's hand and had to grab it when John could only get it off the bed so far. He nodded at Lorne and took his leave.

"Lorne?"

"Yes sir?"

"Sit, will you? You're making me nervous."

"Me? Making you nervous? That'll be the day." Evan huffed out with a laugh as he sat in the chair by his CO's bed.

"So, tell me what's been going on? What've I missed?"

"Well, when Kanaan was still in control, I spent most of my time breaking up fights between ATA gene carriers and non-carriers, military or civilian, didn't matter. Once the situation was under control, I had to squash the 'I told you so's." He paused. "There are many who would like to tell you they were sorry, even if they never did anything directly to you." He knew what would be coming next.

"And the ones who did do something directly to me?"

Lorne sighed. "Jennings, Manning, Johnson and Delaney. They confessed immediately after the doc's retrovirus worked, even placed themselves in custody."

"You know it wasn't their fault?"

"I know that, you know that, but try convincing them of that! They all admire and like you, they can't figure out how they could've done what they did."

"Did you tell them about Kanaan?"

"Of course, doesn't seem to have made a difference."

John sighed. "Where are they now?"

"Holding cells."

"What? Why would you leave them there?"

"I didn't! The door isn't even locked! They just won't leave, except to sit with you and cover their duty roster. Once they were off duty, each one headed back to the holding cells. Since you finally woke up, not one of them has left there." Lorne had tried to get through to them, but not one would budge.

"They all disobeyed your direct orders to return to duty?" This bothered him more than the beating. Lorne's eyes dropped and he fidgeted in his chair. "Lorne?"

Lorne stared at the privacy screen across from him, not meeting his CO's eyes. "Well..."

"Evan, what's up?"

"I may not have given them a direct order to return to duty."

"Why?"

He risked a look at Sheppard and saw only curiosity, no condemnation or disappointment. "I...I guess I empathized with them. When I was taken over by the crystal entity and was sleep walking, I really thought you were a replicator and wanted to destroy you."

"But you didn't."

"No, I was lucky. If things had gone differently..."

"They didn't and even if they had, you weren't responsible."

"I know that but I can imagine how I would have felt and I could see myself feeling exactly like these men do. I couldn't bring myself to order them to do something I would have refused to do."

John sighed. "Okay, bring them here to me, in shackles."

"Sir?"

"Just do it Lorne!"

Evan reached up and activated his comms. "Sgt. Stackhouse?"

"Yes sir?"

"Would you please bring the prisoners up to the infirmary, in chains please?"

"With pleasure sir!" Lorne grimaced at the pleased tone of the younger man's voice.

"Evan?" He was frustrated that he didn't have his comms and had to rely on someone else to tell him what was going on.

"Sorry sir, Sgt. Stackhouse seems to have taken this very personally. He wants all four to be brought up on charges and send back to Earth immediately, even knowing they weren't in control of themselves."

"He's a good kid."

"I know that John, I just wish he'd be a little less combative about this."

"I'll talk to him too." John had a feeling he would be dealing with the fallout from this for a long time to come. While they waited, his 2IC brought him up to date on everything that had gone in Atlantis while he was out of commission, including the latest gossip.

"She did what?" John asked, laughing at a bit of gossip about a love triangle that was forming between three scientists, when Stackhouse arrived with his charges. None of the four would look him in the face, although all four stood ramrod straight. "Okay, everyone else out." Stackhouse looked mutinous but Lorne dragged him out of the infirmary. John stayed quiet, waiting them out.

Finally Jennings couldn't stand it any longer and raised his head. "Sir, I…I don't know what to say or how to apologize! I want you know that we'll accept any punishment you deem necessary."

"Captain, do you harbor any ill feelings towards me right now? Do you feel I'm unfit to command?"

"No sir! Just the opposite in fact! You're the best CO I've ever had! I've enjoyed working for you here on Atlantis, more that anyone I've ever worked under. I'll miss it."

"Then you accept my authority?"

"Yes sir!"

John looked at the others. "Do you all feel that way?"

A chorus of 'yes sir's met his question. "Very well. I've decided what your punishment should be." All four waited, looking downcast. "You will be forced to stay on Atlantis and continue to work under me. You will understand that nothing that happened was within your control. You will also all meet with Dr. Straub, the base psychologist, who will, hopefully, help you to see that this was not your fault. I've already forgiven my team for what happened. Can you accept that I don't hold you accountable?"

"Sir, we did what we did."

"Yes, you did. And I did what I did. I attacked Teyla in the gym when I was mutating into a bug, I tried to kill Dr. Weir while under the control of Thalen, do you think I should be sent away? Made to pay for what I did when I wasn't in control of myself? If you believe you need to be punished, then I'll submit myself for the same punishment and resign my command here."

"No, sir! You can't do that!" Manning burst out. He'd been here from the beginning, coming to Atlantis under the command of Colonel Sumner, a man he'd respected but had found to be rigid. He doubted they'd all still be alive if Sumner had remained in command. He'd been on Athos when they'd first met the Athosians, trying to find a place to bring their people to as the city was failing but, instead, had brought the Wraith down on them. He'd seen Sheppard refuse to give up on the people who'd been culled as he fought with Dr. Weir to be allowed to mount a rescue, and rescue most of them he did. He'd heard about what had happened during the storm that had forced all of them off the city, leaving it open to the Genii and Kolya to almost seize control. The man in the bed could think on his feet and adjust to any situation at hand, better than anyone he'd ever seen. That was what was needed on Atlantis, not someone like Caldwell, who he knew would be on the short list to take over. In fact, he was pretty sure Caldwell was the list.

"Very well, that's your choice, do you accept your punishment or do I resign?" He raised an eyebrow.

"Sir, why would you do that?" Asked Johnson, the one with the least tenure on Atlantis. He'd heard the tales of the things the Colonel and his team had done, but he'd taken a lot of it with a grain of salt. He had, however, seen some things with his own eyes that had cemented his admiration of his CO.

"I would do that because I've been where you are. I was not held accountable for things that were out of my control. How much of a hypocrite would I be to hold you to a higher standard?"

Jennings pulled in a deep breath, finally daring to hope. "Sir, I would like to state I'll take the _punishment_ of working under you for as long as you'll have me." The others nodded. John hid the relief he felt. He'd have had to follow through if his men hadn't accepted his offer and the last thing he wanted was to ever leave here.

"Very well." He raised his voice. "Stackhouse?"

The man popped into the infirmary, confirming John's instinct that he hadn't gone far, regardless of his orders. "Sergeant, please release these men from their bonds."

"Sir?"

"You heard me, they are to be released and allowed to go back to their duties."

The man stiffened but did as he was ordered. He undid the locks on each man silently and watched as each saluted their CO and left the area. He started to follow when John called him back. "Sergeant?"

"Yes sir?"

"Look, Phil, I know you don't agree with me and I'm honored that you feel so strongly about punishing those who hurt me, but you have to know they wouldn't have done what they did under normal circumstances."

"Permission to speak freely sir?"

"Always."

Stackhouse started to pace. "With all due respect, Colonel, you didn't see what they did to you! I was on first watch when we were afraid to leave you unguarded. You looked like there wasn't an inch of your body that wasn't damaged! How can I trust someone who did that?"

John sighed. "Do you trust me?"

"Yes sir! With my life sir!"

"You know the things I've done when I wasn't myself?"

"Well, yes sir, but…"

"No buts son, they are not accountable for what happened any more than I was. I'm hoping you can trust me enough to come to terms with that. I need you here at my side."

Stackhouse puffed up a little at the compliment, as John had hoped. "I'll do my best sir!"

"That's good to hear. Any time you find yourself doubting that, come and find me. My door is always open."

"Thank you sir!"

"You're welcome. Now, dismissed. I'm thinking there's a nap in my very near future." He winked at the younger man and was relieved to see an answering smirk. Stackhouse nodded and left the infirmary. John leaned back and sighed, exhausted.

"Ye did good there, laddie." John turned his head to find the doctor coming around the privacy curtain, stethoscope around his neck.

"Carson? Eavesdropping?"

"I was on my way to check up on ye and stopped when I heard voices. Major Lorne had filled me in on what was going on with those men and I was curious to see how ye dealt with it." He was unrepentant about overhearing the conversation between the CO and his men.

"Well, thanks for the vote of confidence. I have to admit, I was a little worried they wouldn't take me up on my offer and I'd have to follow through and resign."

"Ach, I doubt there was ever a chance of that. Those lads just needed to hear it from your lips, no one else could make them accept what they'd done."

"I hope they can get past this."

"Well, they've taken the first step. Now, let's see how ye're doing." John lay back and submitted to the doctor's exam, falling asleep before it was over.

~,~,~,~

He was still sleeping when the light came again. This time he was prepared. "Atlantis?"

"Yes, I am here John."

"It's good to see you again."

"I am glad to see you as well. Are you feeling better?"

"I am. Thank you!"

"For what?" He watched the knowing smile he remembered, grace his mother's face.

"For giving me the kick in the pants I needed. I should've known that my team would never willingly turn against me without good reason. I was hiding for no good reason."

"I am pleased that you feel that way."

"I'm glad you're here. Does that mean we'll be able to communicate from now on?"

"Yes, you have taken the steps forward to allow us to speak at will. If you continue like this, we will be able to speak even when you are awake."

"I'd really like that."

"As would I. Your friends are greatly relieved. They missed you."

"I missed them too." He paused. "You said there have been others before me?"

"Yes, John, many others over the years, although there was a long, lonely time while I slumbered beneath the waters. Your appearance was most welcome."

He smiled. "I felt like I was coming home as soon as I stepped through the gate. Was that you?"

"Yes, your presence was so strong when you first stepped foot on me. I had never felt the connection so strongly, so quickly, even with my makers, those you term the ancients."

He grinned at her and was surprised at the answering grin. Atlantis seemed as human as him. "I'm glad to see you looking so pleased." He smirked.

"You have done well. I watched while you dealt with the men who grievously harmed you. It was masterfully done. I am not sure if I would have been as generous."

Even in his dreams, Sheppard blushed at the praise. "I was lucky and I do believe they are innocent of any wrongdoing. Still, it could easily have gone the other way."

"No, John, it could not have. You have the hearts of most here in the city. Those that do not agree, have their own issues. While most thought your Dr. Weir was the heart, many believe that you are the soul of your people. With her passing, you have taken on both roles."

"Um, well, thanks."

Atlantis shook her head, her smile widening. Before him, the ones she connected with had all been of the race of her makers. Sure of themselves and believing that they were always in the right. Never admitting to their mistakes. John Sheppard had shown her a different side of the species known as human. She found she liked this form better.

"Sleep now, John, we will speak again soon." The light faded as he drifted back into a deep sleep.

When he awoke again, the infirmary was quiet and in near darkness. He sensed her presence before she said anything, he always knew when she was near. "John?"

"Hi Teyla, it's good to see you! Where's Torren?" He saw she was alone, instantly missing the presence of the toddler.

"Ronon and Rodney are watching him. I asked to be able to come here to talk to you alone."

John sighed. "Are you going to apologize now? Seems like that's all anyone wants to do these days."

Her chin quivered and he worried that he'd hurt her feelings. "John, I know in my head that I am not to blame for what happened, but in my heart I find it hard to forgive myself."

He reached out a hand to her, already stronger than he had been when he'd first come out of it. She took it and held on tight. "Teyla, you trusted Kanaan, there's no way you could've known what he was capable of."

"I was the one who brought him here! I was the one who requested he be able to live on Atlantis with us. If I had left it alone, if I had just let him stay with our people on New Athos, he would not have been able to do what he did! You almost…you almost died because of him. I do not think I could ever have forgiven myself if things had turned out differently."

"He's the father of your son, Teyla. He's someone you've known all your life, someone you trusted. How could you have known this would happen?" He squeezed her hand and smiled at her. Suddenly he heard Atlantis in his head, remembering the things she had said to him. He knew Teyla was the one who was waiting for him with love. It was time for him to stop hiding his feelings. "Teyla? I…" He paused, still not comfortable with expressing his feelings, but knowing Atlantis was right, it didn't serve him well. He took a deep breath. "I need to tell you something."

"John, I need to tell you something as well and I would like to say it now, before I lose my courage."

"You're one of the bravest people I've ever met, I find it hard to believe you're afraid to tell me anything."

"I am afraid of this. Afraid it will change everything but I cannot keep it to myself any longer."

"Teyla?" He knew what she was going to say and was determined to say it first. His heart full, brimming with confidence based on his conversation with his city, he put himself out there.

"Yes John?"

"I love you too."

~,~,~,~

A/N2 – I have no idea what Sgt. Stackhouse's first name is and couldn't find it on the internet anywhere, so I went with Phil. Honus47 will know who that is! If someone knows what it really is, let me know and I'll update it.


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